Author: bugman
Date: Thu Jan 22 16:34:06 2015
New Revision: 27268
URL: http://svn.gna.org/viewcvs/relax?rev=27268&view=rev
Log:
Added the NUC 4.4 nucleotide substitution matrix from
ftp://ftp.ncbi.nih.gov/blast/matrices/.
Uracil was added to the table as a copy to T.
Modified:
trunk/lib/sequence_alignment/substitution_matrices.py
Modified: trunk/lib/sequence_alignment/substitution_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence_alignment/substitution_matrices.py?rev=27268&r1=27267&r2=27268&view=diff
==============================================================================
--- trunk/lib/sequence_alignment/substitution_matrices.py (original)
+++ trunk/lib/sequence_alignment/substitution_matrices.py Thu Jan 22
16:34:06 2015
@@ -34,6 +34,37 @@
[-1, -1, -1, 1]
], int16)
+
+# This matrix was created by Todd Lowe 12/10/92
+#
+# Uses ambiguous nucleotide codes, probabilities rounded to
+# nearest integer
+#
+# Lowest score = -4, Highest score = 5
+#
+# Taken from ftp://ftp.ncbi.nih.gov/blast/matrices/NUC.4.4.
+NUC_4_4_SEQ = 'ATGCSWRYKMBVHDNU'
+NUC_4_4 = array([
+ # A, T, G, C, S, W, R, Y, K, M, B, V, H, D, N,
U
+ [ 5, -4, -4, -4, -4, 1, 1, -4, -4, 1, -4, -1, -1, -1, -2,
-4], # A
+ [-4, 5, -4, -4, -4, 1, -4, 1, 1, -4, -1, -4, -1, -1, -2,
5], # T
+ [-4, -4, 5, -4, 1, -4, 1, -4, 1, -4, -1, -1, -4, -1, -2,
-4], # G
+ [-4, -4, -4, 5, 1, -4, -4, 1, -4, 1, -1, -1, -1, -4, -2,
-4], # C
+ [-4, -4, 1, 1, -1, -4, -2, -2, -2, -2, -1, -1, -3, -3, -1,
-4], # S
+ [ 1, 1, -4, -4, -4, -1, -2, -2, -2, -2, -3, -3, -1, -1, -1,
1], # W
+ [ 1, -4, 1, -4, -2, -2, -1, -4, -2, -2, -3, -1, -3, -1, -1,
-4], # R
+ [-4, 1, -4, 1, -2, -2, -4, -1, -2, -2, -1, -3, -1, -3, -1,
1], # Y
+ [-4, 1, 1, -4, -2, -2, -2, -2, -1, -4, -1, -3, -3, -1, -1,
1], # K
+ [ 1, -4, -4, 1, -2, -2, -2, -2, -4, -1, -3, -1, -1, -3, -1,
-4], # M
+ [-4, -1, -1, -1, -1, -3, -3, -1, -1, -3, -1, -2, -2, -2, -1,
-1], # B
+ [-1, -4, -1, -1, -1, -3, -1, -3, -3, -1, -2, -1, -2, -2, -1,
-4], # V
+ [-1, -1, -4, -1, -3, -1, -3, -1, -3, -1, -2, -2, -1, -2, -1,
-1], # H
+ [-1, -1, -1, -4, -3, -1, -1, -3, -1, -3, -2, -2, -2, -1, -1,
-1], # D
+ [-2, -2, -2, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
-2], # N
+ [-4, 5, -4, -4, -4, 1, -4, 1, 1, -4, -1, -4, -1, -1, -2,
5], # U
+], int16)
+
+
BLOSUM62_SEQ = 'ARNDCQEGHILKMFPSTWYVBZX*'
BLOSUM62 = array([
# A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W,
Y, V, B, Z, X, *
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